Single-cell analysis of long non-coding RNAs in the developing human neocortex

Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that can regulate molecular and cellular processes in brain development and disease. LncRNAs exhibit cell type- and tissue-specific expression, but little is known about the expression and function of lncRNAs in the developing human brain. Furthermore, it has been unclear whether lncRNAs are highly expressed in subsets of cells within tissues, despite appearing lowly expressed in bulk populations.

Researchers at the University of California, San Francisco use strand-specific RNA-seq to deeply profile lncRNAs from polyadenylated and total RNA obtained from human neocortex at different stages of development, and they apply this reference to analyze the transcriptomes of single cells. While lncRNAs are generally detected at low levels in bulk tissues, single-cell transcriptomics of hundreds of neocortex cells reveal that many lncRNAs are abundantly expressed in individual cells and are cell type-specific. Notably, LOC646329 is a lncRNA enriched in single radial glia cells but is detected at low abundance in tissues. CRISPRi knockdown of LOC646329 indicates that this lncRNA regulates cell proliferation.

Single-cell transcriptomics of lncRNA expression

a Schematic of single-cell microfluidic capture and integration of transcriptome reference generated from bulk tissue RNA-seq to conduct cell-type identification and lncRNA analysis. Previously captured cells from Pollen et al.were also included. b Distributions of median lncRNA expression to median mRNA expression ratios (lncRNA:mRNA) in bulk tissues, in silico merged single cells, and single cells from the developing neocortex. c Proportion of neocortex cells that expressed each lncRNA (blue) and mRNA (red), separated by maximum expression in single cells. d Same as in (c) but grouped by maximum expression quantile of the set of all transcripts (lncRNA and mRNA combined). Green squares, housekeeping genes; black triangles, ERCC Spike-In Controls

The discrete and abundant expression of lncRNAs among individual cells has important implications for both their biological function and utility for distinguishing neural cell types.